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The anatomy of successful computational biology software.
Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. Altschul S, et al. Among authors: gentleman r. Nat Biotechnol. 2013 Oct;31(10):894-7. doi: 10.1038/nbt.2721. Nat Biotechnol. 2013. PMID: 24104757 Free PMC article. No abstract available.
Orchestrating high-throughput genomic analysis with Bioconductor.
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M. Huber W, et al. Among authors: gentleman r. Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Nat Methods. 2015. PMID: 25633503 Free PMC article. Review.
Top-down standards will not serve systems biology.
Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N. Quackenbush J, et al. Among authors: gentleman r. Nature. 2006 Mar 2;440(7080):24. doi: 10.1038/440024a. Nature. 2006. PMID: 16511469 No abstract available.
Bioconductor: open software development for computational biology and bioinformatics.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Gentleman RC, et al. Genome Biol. 2004;5(10):R80. doi: 10.1186/gb-2004-5-10-r80. Epub 2004 Sep 15. Genome Biol. 2004. PMID: 15461798 Free PMC article.
Graphs in molecular biology.
Huber W, Carey VJ, Long L, Falcon S, Gentleman R. Huber W, et al. Among authors: gentleman r. BMC Bioinformatics. 2007 Sep 27;8 Suppl 6(Suppl 6):S8. doi: 10.1186/1471-2105-8-S6-S8. BMC Bioinformatics. 2007. PMID: 17903289 Free PMC article. Review.
Prediction and Quantification of Splice Events from RNA-Seq Data.
Goldstein LD, Cao Y, Pau G, Lawrence M, Wu TD, Seshagiri S, Gentleman R. Goldstein LD, et al. Among authors: gentleman r. PLoS One. 2016 May 24;11(5):e0156132. doi: 10.1371/journal.pone.0156132. eCollection 2016. PLoS One. 2016. PMID: 27218464 Free PMC article.
84 results